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Project Information
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jmzquantml -- A Java API for mzQuantML
Generaljmzquantml is a JAVA API for reading and writing mzQuantML file
which is designed for reording quantitative proteomic data and
meta-data.
Download JAR file
As Googlecode has terminated the download service on January 2014, new release after version 1.0.0-1.0.3 cannot be found in download section from left column. The latest jar file can be downloaded from http://code.google.com/p/jmzquantml/source/browse/#svn%2Fmaven%2Frepo%2Fuk%2Fac%2Fliv%2Fjmzquantml. Before download, refer to "release notes" for latest news.
Documentations
Here are the API documentation links to all API versions. http://jmzquantml.googlecode.com/svn/trunk/src/docs/api/index.htm How to use jmzquantml artifact in maven
jmzquantml artifact is currently using Googlecode host as its maven
repository. To use it, add the following to your POM:
First, add jmzquantml dependency (check the latest version):
<dependency>
<groupId>uk.ac.liv</groupId>
<artifactId>jmzquantml</artifactId>
<version>1.0.0-1.0.5</version>
</dependency>Second, add wagon-svn extension (current version 1.12) in <build> tag:
<extensions>
<extension>
<groupId>org.jvnet.wagon-svn</groupId>
<artifactId>wagon-svn</artifactId>
<version>1.12</version>
</extension>
</extensions>Finally, add plugin repository and jmzquantml repository:
<pluginRepositories>
<pluginRepository>
<id>maven2-repository.dev.java.net</id>
<name>Java.net Repository for Maven</name>
<url>http://download.java.net/maven/2/</url>
</pluginRepository>
</pluginRepositories>
<repositories>
<repository>
<id>jmzquantml-maven-repo</id>
<name>Maven Repository for jmzquantml release</name>
<url>http://jmzquantml.googlecode.com/svn/maven/repo</url>
</repository>
</repositories>
Examples
To help users to familiarise with the API, we have generated some example classes to illustrate the most important features. They can be found from here.
Citation
The paper of jmzquantml API has been published in Proteomics. If you would like to cite jmzquantml in your paper, please use the following citation: PlainQi, D., Krishna, R. and Jones, A. R. (2014), The jmzQuantML programming interface and validator for the mzQuantML data standard. Proteomics, 14: 685–688. doi: 10.1002/pmic.201300281 Bibtex
@article {QI14:PROTEOMICS,
author = {Qi, Da and Krishna, Ritesh and Jones, Andrew R},
title = {The jmzQuantML programming interface and validator for the mzQuantML data standard},
journal = {PROTEOMICS},
volume = {14},
number = {6},
issn = {1615-9861},
url = {http://dx.doi.org/10.1002/pmic.201300281},
doi = {10.1002/pmic.201300281},
pages = {685--688},
keywords = {Bioinformatics, Java API, mzQuantML, Proteomics Standards Initiative, XML},
year = {2014},
} Contact
Dr Da Qi (D.Qi at liverpool.ac.uk , replace at with @) Dr Andy Jones (Andrew.Jones at liverpool.ac.uk, replace at with @) last update: 22/08/2014
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